Hello everyone,
This issue has been driving me nuts for a while and I thought I would add my own experience. I am currently using the latest versions of iOS9 on an iPhone 6+ and an iPad Mini 3 (both 128 GB and purchased late 2014). I have been using the photos app synced via iTunes 12.3.1.23 to store the same set of 10,862 photos on each of these devices. I do not use iCloud or iCloud Drive for photos. All apps and firmware are up to date with the latest versions available (as of 16th November 2016). This post is a bit number heavy so apologies in advance.
I cleaned-out my iPad Mini this morning, reset everything and set-up as a 'new iPad'. FYI I added 55.75 GB audio, 24.22 GB video, 1.58 GB apps, 1.21 GB documents and data. I left photos to the very last. That's when the fun began. While the photo sync was in progress the iTunes status bar reported that I had added 21.76 GB of photos. 'Other' was measured at 1.53GB and there was 8.5 GB of free space. As soon as the last photo had been copied and the sync was complete the status bar showed no photos, 'Other' shrank to 1.23 GB. The Free space had grown to 28.19 GB!!! Still connected to iTunes, I opened the iPad and checked that the photos had transferred. They were all there.
Then I clicked sync again (without the iPad being ejected after the initial sync): photos 21.76 GB; Other 1.53 GB; free space 8.47 GB. Great while it was being synced but at the end: NO photos reported; Other reported as 19.44 GB; free space 9.98 GB. Er...What?
I ejected the iPad. All items were there. I checked the usage - all the numbers for songs, videos, photos were correct. Free space was reported as 9.6 GB.
I reconnected the iPad to iTunes: it reported 0 GB of photos, 19.44 GB 'other', 9.98 GB of free space. When I clicked 'sync' this changed to 9.30 GB of photos, 19.74 GB 'other', 2.72 GB of free space while the sync was in progress. When the sync completed it reverted to 0 GB of photos, 19.44 GB 'other', 9.98 GB of free space. The growing and shrinking 'free' space and bogus reporting of 'Other' is very irritating and limiting. I have almost 10 GB of free space before I click sync then only 2.72 while the sync is on.
The problem has been ongoing since the Photos app first appeared. I miss iPhoto.